Rhisat2
This is the development version of Rhisat2; for the stable release version, see Rhisat2.
All Bioconductor versions of Rhisat2
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9
R Wrapper for HISAT2 Aligner
Bioconductor version: 3.24 · Package version: 1.29.1
An R interface to the HISAT2 spliced short-read aligner by Kim et al. (2015). The package contains wrapper functions to create a genome index and to perform the read alignment to the generated index.
Author: Charlotte Soneson [aut, cre] 
Maintainer: Charlotte Soneson <charlottesoneson at gmail.com>
Citation
From within R, enter citation("Rhisat2"):
Charlotte Soneson. Rhisat2: R Wrapper for HISAT2 Aligner. doi:10.18129/B9.bioc.Rhisat2, R package version 1.29.1, https://bioconductor.org/packages/Rhisat2.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("Rhisat2")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.29.1 |
| License | GPL-3 |
| URL | https://github.com/fmicompbio/Rhisat2 |
| Bug Reports | https://github.com/fmicompbio/Rhisat2/issues |
| System Requirements | GNU make |
| Last updated | 2026-07-29 |
| In Bioconductor since | BioC 3.9 (R-3.6) (7 years) |
| Downloads rank | 954 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Alignment, Sequencing, Software, SplicedAlignment |
| Package Short Url | https://bioconductor.org/packages/Rhisat2/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("Rhisat2")| Aligning reads with Rhisat2 | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | Rhisat2_1.29.1.tar.gz |
| Windows binary (x86_64) | Rhisat2_1.29.1.zip |
| macOS binary (arm64) | Rhisat2_1.29.1.tgz |
| macOS binary (x86_64) | Rhisat2_1.29.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/Rhisat2 |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Rhisat2 |
| Package Downloads Report | Download Stats |